Contacts of the helix formed by residues 365 - 379 (chain J) in PDB entry 1QDU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 365 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J GLY 3.3 4.9 + - - -
364J ASP* 1.3 72.2 - - - +
366J ILE* 1.3 64.7 + - - +
367J LEU* 2.6 47.7 + - - +
368J THR* 2.9 38.4 + - - +
369J ILE* 3.0 9.9 - - - +
397J LYS* 3.4 47.8 + - + -
398J LEU 3.7 18.7 + - - +
399J VAL* 4.6 2.9 - - + -
367L LEU* 5.9 0.2 - - - +
397L LYS* 4.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279I VAL* 6.2 0.4 - - + -
281I PHE* 4.7 14.8 - - + -
328J LEU* 3.4 28.9 - - + -
353J LEU* 5.2 1.8 - - + -
357J LEU* 4.9 9.6 - - + -
364J ASP 3.6 1.0 + - - -
365J ASP* 1.3 78.4 + - - +
367J LEU* 1.3 65.3 + - + +
369J ILE* 3.4 18.3 + - + +
370J LEU* 2.8 45.6 + - + +
394J LEU* 4.4 2.2 - - + -
398J LEU* 2.7 40.2 + - + +
400J PHE* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328J LEU* 4.8 2.9 - - + -
365J ASP* 2.6 29.2 + - - +
366J ILE* 1.3 84.3 - - + +
368J THR* 1.3 56.4 + - - +
370J LEU* 3.0 14.3 + - + +
371J THR* 2.8 33.7 + - - -
392J PHE* 4.1 32.5 - - + -
394J LEU* 4.5 15.3 - - + -
396J LYS 5.8 0.9 - - - +
397J LYS* 6.0 3.6 - - + +
398J LEU 5.9 1.1 - - - +
367L LEU* 4.2 30.3 - - + -
368L THR* 6.1 0.7 - - - -
371L THR* 3.6 24.0 - - + +
392L PHE* 4.3 11.8 - - + -
397L LYS* 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J ARG* 3.8 29.4 - - - +
364J ASP* 4.1 6.7 - - + +
365J ASP* 2.9 29.3 + - - +
367J LEU* 1.3 78.4 - - - +
369J ILE* 1.3 66.4 + - - +
371J THR* 2.9 18.5 + - - -
372J GLU* 3.2 10.9 + - - +
397J LYS* 5.9 0.3 - - - -
150K ASP* 4.1 16.4 - - + +
397L LYS* 3.3 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353J LEU* 4.5 7.0 - - + +
356J SER* 3.6 26.7 - - - +
357J LEU* 4.0 19.1 - - + +
360J ARG* 3.5 29.2 - - + -
361J CYS* 4.8 12.3 - - - +
364J ASP* 2.8 38.1 - - + +
365J ASP 3.0 20.2 + - - +
366J ILE* 3.7 14.6 - - + +
368J THR* 1.3 79.1 - - - +
370J LEU* 1.3 65.2 + - - +
371J THR 3.1 0.5 + - - -
372J GLU* 3.1 8.9 + - - +
373J VAL* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I PHE* 4.6 12.6 - - + -
328J LEU* 3.9 31.6 - - + -
330J GLY* 5.0 2.5 - - - -
349J TYR* 3.8 24.2 - - + +
353J LEU* 4.7 6.3 - - + -
366J ILE* 2.8 30.9 + - + +
367J LEU* 3.4 11.7 - - + +
369J ILE* 1.3 73.9 - - - +
371J THR* 1.3 61.2 + - - +
373J VAL* 3.4 17.8 + - + +
374J ASN* 3.1 24.0 + - - +
389J PRO* 3.8 34.8 - - + +
392L PHE* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 371 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J LEU 2.8 20.0 + - - -
368J THR* 2.9 11.3 + - - -
370J LEU* 1.3 74.5 - - - +
372J GLU* 1.3 58.1 + - - +
374J ASN* 2.8 27.7 + - - +
375J TYR* 2.9 10.9 + - - +
367L LEU* 3.9 18.2 - - + +
392L PHE* 4.1 7.8 - - - -
394L LEU* 3.7 11.8 - - + +
395L ARG 3.6 3.8 - - - +
396L LYS* 3.4 42.8 - - - +
397L LYS* 4.4 6.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J SER* 3.5 25.8 + - - +
359J GLU* 4.8 6.6 - - - +
360J ARG* 2.8 49.0 + - - +
368J THR 3.2 6.5 + - - +
369J ILE* 3.1 8.9 + - - +
371J THR* 1.3 76.6 - - - +
373J VAL* 1.3 59.6 + - - +
375J TYR* 2.8 12.4 + - + +
376J GLU* 2.8 58.0 + - + +
395L ARG 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 373 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J TYR* 3.8 29.4 - - + -
352J SER* 3.6 21.1 - - - +
353J LEU* 3.8 22.9 - - + +
356J SER* 3.7 20.0 - - - +
369J ILE* 3.0 21.6 + - + +
370J LEU* 3.4 12.8 - - + +
371J THR 3.1 0.2 - - - -
372J GLU* 1.3 76.3 - - - +
374J ASN* 1.3 60.4 + - - +
376J GLU* 4.4 1.1 - - - -
377J VAL* 2.8 43.5 + - + +
387J PRO* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370J LEU 3.1 11.5 + - - +
371J THR 2.8 14.0 + - - +
373J VAL* 1.3 76.9 - - - +
375J TYR* 1.3 54.6 + - - +
377J VAL* 4.1 1.7 - - - +
378J SER* 2.5 34.1 + - - -
386J MET* 3.4 15.2 - - + +
387J PRO* 3.2 33.3 + - - +
389J PRO* 3.7 10.6 - - - +
392L PHE* 3.4 23.8 - - - -
393L THR* 3.7 13.9 - - - +
394L LEU 3.1 23.8 + - - +
395L ARG* 3.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 375 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I ASP* 3.0 33.3 - - + +
371J THR 2.9 4.4 + - - -
372J GLU* 2.8 16.0 + - + +
374J ASN* 1.3 76.1 - - - +
376J GLU* 1.3 71.5 + - - +
378J SER* 2.6 32.1 + - - -
379J ASN* 3.4 23.4 + - - -
151K LYS* 3.9 37.2 - - + -
319L ARG* 3.8 13.0 + - - -
395L ARG* 3.5 53.5 - - + +
396L LYS* 5.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352J SER* 3.7 20.2 - - - +
355J GLN* 5.6 8.5 + - - +
356J SER* 4.7 4.3 - - - +
372J GLU* 2.8 51.1 + - + +
373J VAL* 4.1 0.4 - - - +
375J TYR* 1.3 87.1 - - - +
377J VAL* 1.3 61.3 + - - +
379J ASN* 3.3 20.2 + - - +
381J LYS* 3.7 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348J TRP* 4.1 24.3 - - + +
349J TYR* 4.5 2.7 - - - -
352J SER* 3.8 15.7 - - - +
373J VAL* 2.8 40.1 + - + +
376J GLU* 1.3 75.7 - - - +
378J SER* 1.3 61.7 + - - +
381J LYS* 3.3 23.2 + - - +
385J GLN* 3.6 42.1 + - + +
387J PRO* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 378 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374J ASN 2.5 20.0 + - - -
375J TYR 2.6 19.1 + - - -
377J VAL* 1.3 72.6 - - - +
379J ASN* 1.3 56.5 + - - -
384J LYS* 2.9 31.1 + - - +
385J GLN 4.3 4.1 + - - -
386J MET* 3.8 9.0 - - - +
320L TYR 3.7 3.5 - - - +
321L ILE* 4.8 0.7 - - - -
322L PRO* 3.7 22.4 - - - +
395L ARG* 3.4 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 379 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I ASP* 4.9 4.5 - - - +
375J TYR* 3.4 46.2 + - - -
376J GLU* 3.3 12.8 + - - +
378J SER* 1.3 78.2 - - - +
381J LYS* 1.3 75.0 + - - +
384J LYS* 3.9 4.4 + - - +
319L ARG* 4.3 17.4 + - - +
320L TYR 3.9 11.0 - - - +
321L ILE* 4.5 1.2 - - - +
395L ARG* 4.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il